/dports/science/jmol/jmol-14.32.7/src/org/jmol/modelset/ |
H A D | AtomIteratorWithinModelSet.java | 35 private BS bsModels; field in AtomIteratorWithinModelSet 37 public AtomIteratorWithinModelSet(BS bsModels) { in AtomIteratorWithinModelSet() argument 38 this.bsModels = bsModels; in AtomIteratorWithinModelSet() 52 if ((modelIndex = bsModels.nextSetBit(iModel)) < 0 in set()
|
H A D | Trajectory.java | 169 BS bsModels = new BS(); in getModelsSelected() local 173 bsModels.set(t); in getModelsSelected() 177 return bsModels; in getModelsSelected() 274 public void setBaseModels(BS bsModels) { in setBaseModels() argument 276 if (bsModels.get(i) && ms.am[i].isTrajectory) in setBaseModels() 277 bsModels.set(ms.am[i].trajectoryBaseIndex); in setBaseModels()
|
H A D | ModelSet.java | 317 if (bsModels.get(i)) in setTrajectoryBs() 673 if (bsModels.get(i)) { in includeAllRelatedFrames() 681 bsModels.set(i); in includeAllRelatedFrames() 700 for (int i = bsModels.nextSetBit(0); i >= 0; i = bsModels.nextSetBit(i + 1)) in deleteModels() 757 if (!bsModels.get(i)) { in deleteModels() 2046 for (int i = bsModels.nextSetBit(0); i >= 0; i = bsModels in getSelectedAtomIterator() 2079 if (bsModels == null) in getModelAtomBitSetIncludingDeletedBs() 2082 for (int i = bsModels.nextSetBit(0); i >= 0; i = bsModels in getModelAtomBitSetIncludingDeletedBs() 3357 for (int i = bsModels.nextSetBit(0); i >= 0; i = bsModels.nextSetBit(i + 1)) in setFrameDelayMs() 3409 if (bsModels == null || bsModels.get(i)) { in getAuxiliaryInfo() [all …]
|
H A D | BondCollection.java | 494 BS bsModels = new BS(); in assignAromaticBondsBs() local 500 bsModels.set(bond.atom1.mi); in assignAromaticBondsBs() 511 for (int i = bsModels.nextSetBit(0); i >= 0; i = bsModels.nextSetBit(i + 1)) in assignAromaticBondsBs()
|
/dports/science/jmol/jmol-14.32.7/src/org/jmol/modelsetbio/ |
H A D | BioModelSet.java | 164 setAllDefaultStructure(bsModels); in calculateAllStructuresExcept() 165 for (int i = bsModels.nextSetBit(0); i >= 0; i = bsModels.nextSetBit(i + 1)) in calculateAllStructuresExcept() 203 BS bsModels = modelsOf(bsAtoms, bsModified); in getAllDefaultStructures() local 205 for (int i = bsModels.nextSetBit(0); i >= 0; i = bsModels.nextSetBit(i + 1)) in getAllDefaultStructures() 573 for (int i = bsModels.nextSetBit(0); i >= 0; i = bsModels.nextSetBit(i + 1)) in setAllConformation() 590 BS bsModels = ms.getModelBS(bs, false); in setAllProteinType() local 591 setAllDefaultStructure(bsModels); in setAllProteinType() 995 BS bsModels = BS.newN(ms.mc); in modelsOf() local 1004 bsModels.set(modelIndex); in modelsOf() 1007 return bsModels; in modelsOf() [all …]
|
/dports/science/jmol/jmol-14.32.7/src/org/jmol/shapespecial/ |
H A D | Ellipsoids.java | 53 public boolean checkObjectHovered(int x, int y, BS bsModels) { in checkObjectHovered() argument 56 Ellipsoid e = findPickedObject(x, y, false, bsModels); in checkObjectHovered() 74 BS bsModels, in checkObjectClicked() argument 79 Ellipsoid e = findPickedObject(x, y, false, bsModels); in checkObjectClicked() 108 BS bsModels) { in findPickedObject() argument 118 if (!e.visible || !bsModels.get(e.modelIndex)) in findPickedObject() 510 public void setModelVisibilityFlags(BS bsModels) { in setModelVisibilityFlags() argument 517 setVis(simpleEllipsoids, bsModels, atoms); in setModelVisibilityFlags() 518 setVis(atomEllipsoids, bsModels, atoms); in setModelVisibilityFlags()
|
H A D | Draw.java | 682 BS bsModels = vwr.getVisibleFramesBitSet(); in setDrawing() local 684 if (bsModels.get(iModel) && setPoints(iModel, -1)) { in setDrawing() 1147 public void setModelVisibilityFlags(BS bsModels) { in setModelVisibilityFlags() argument 1159 if (m.modelIndex >= 0 && !bsModels.get(m.modelIndex) || m.modelFlags != null in setModelVisibilityFlags() 1160 && !BSUtil.haveCommon(bsModels, m.modelFlags)) { in setModelVisibilityFlags() 1165 m.bsMeshesVisible.and(bsModels); in setModelVisibilityFlags()
|
H A D | Dipoles.java | 676 public void setModelVisibilityFlags(BS bsModels) { in setModelVisibilityFlags() argument 683 dipole.visibilityFlags = ((dipole.modelIndex < 0 || bsModels in setModelVisibilityFlags()
|
H A D | Polyhedra.java | 1463 public void setModelVisibilityFlags(BS bsModels) { in setModelVisibilityFlags() argument 1475 p.visibilityFlags = (p.visible && bsModels.get(p.modelIndex) in setModelVisibilityFlags() 1481 && (p.modelIndex < 0 || bsModels.get(p.modelIndex)) ? vf : 0); in setModelVisibilityFlags()
|
/dports/science/jmol/jmol-14.32.7/src/org/jmol/shapebio/ |
H A D | BioShapeCollection.java | 243 public void setModelVisibilityFlags(BS bsModels) { in setModelVisibilityFlags() argument 246 bsModels = BSUtil.copy(bsModels); in setModelVisibilityFlags() 248 ms.trajectory.setBaseModels(bsModels); in setModelVisibilityFlags() 251 b.modelVisibilityFlags = (bsModels.get(b.modelIndex) ? vf : 0); in setModelVisibilityFlags()
|
/dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/smarter/ |
H A D | AtomSetCollectionReader.java | 190 protected BS bsModels; field in AtomSetCollectionReader 587 bsModels = (BS) val; in initialize() 594 bsModels = (BS) htParams.get("bsModels"); in initialize() 600 if (bsModels != null || firstLastStep != null) in initialize() 602 if (bsModels == null && firstLastStep != null) { in initialize() 609 bsModels = BSUtil.newAndSetBit(firstLastStep[0]); in initialize() 612 bsModels.set(i); in initialize() 615 if (bsModels != null && (firstLastStep == null || firstLastStep[1] != -1)) in initialize() 616 lastModelNumber = bsModels.length(); in initialize() 707 boolean isOK = (bsModels == null ? desiredModelNumber < 1 in doGetModel() [all …]
|
/dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/readers/more/ |
H A D | JcampdxReader.java | 327 BS bsModels = new BS(); in processPeakData() 341 bsModels.set(i); in processPeakData() 357 if (havePeaks && !bsModels.get(i) && id.indexOf(".") >= 0) { in processPeakData()
|
/dports/science/jmol/jmol-14.32.7/src/org/jmol/shape/ |
H A D | TextShape.java | 238 public void setModelVisibilityFlags(BS bsModels) { in setModelVisibilityFlags() argument 241 t.visible = (t.modelIndex < 0 || bsModels.get(t.modelIndex)); in setModelVisibilityFlags()
|
H A D | Shape.java | 135 public void setModelVisibilityFlags(BS bsModels) { in setModelVisibilityFlags() argument
|
H A D | MeshCollection.java | 636 public void setModelVisibilityFlags(BS bsModels) { in setModelVisibilityFlags() argument 646 && (mesh.modelIndex < 0 || bsModels.get(mesh.modelIndex) in setModelVisibilityFlags()
|
H A D | Measures.java | 706 BS bsModels = vwr.getVisibleFramesBitSet(); in setVisibilityInfo() local 720 if (modelIndex >= 0 && !bsModels.get(modelIndex)) in setVisibilityInfo()
|
/dports/science/jmol/jmol-14.32.7/src/org/jmol/shapecgo/ |
H A D | CGO.java | 260 public void setModelVisibilityFlags(BS bsModels) { in setModelVisibilityFlags() argument 264 …m.visibilityFlags = (m.isValid && m.visible && (m.modelIndex < 0 || bsModels.get(m.modelIndex)) ? … in setModelVisibilityFlags()
|
/dports/science/jmol/jmol-14.32.7/src/org/jmol/viewer/ |
H A D | PropertyManager.java | 999 BS bsModels = vwr.ms.getModelBS(vwr in getModelInfo() local 1015 info.put("modelsSelected", bsModels); in getModelInfo() 1019 for (int i = bsModels.nextSetBit(0); i >= 0; i = bsModels.nextSetBit(i + 1)) { in getModelInfo() 1193 BS bsModels = vwr.ms.getModelBS(bsAtoms, true); in getModelExtract() local 1195 String title = vwr.ms.getFrameTitle(bsModels.nextSetBit(0)); in getModelExtract() 1239 ms.trajectory.selectDisplayed(bsModels); in getModelExtract() 1248 for (int i = bsModels.nextSetBit(0); i >= 0; i = bsModels in getModelExtract() 1294 for (int i = bsModels.nextSetBit(0); i >= 0; i = bsModels in getModelExtract() 1863 BS bsModels = vwr.ms.getModelBS(bs, true); in getPdbAtomData() local 1864 int nModels = bsModels.cardinality(); in getPdbAtomData() [all …]
|
H A D | Viewer.java | 3757 public BS getModelUndeletedAtomsBitSetBs(BS bsModels) { in getModelUndeletedAtomsBitSetBs() argument 3758 return slm.excludeAtoms(ms.getModelAtomBitSetIncludingDeletedBs(bsModels), in getModelUndeletedAtomsBitSetBs() 8667 BS bsModels = (bsAtoms == null ? BSUtil.newAndSetBit(modelIndex) in deleteModels() local 8669 BS bsDeleted = ms.deleteModels(bsModels); in deleteModels()
|
H A D | Jmol.properties | 11068 bug fix: CIF reader with bsModels fails
|
/dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/readers/spartan/ |
H A D | SpartanSmolReader.java | 95 modelNumber = (bsModels == null && modelNo != Integer.MIN_VALUE && modelNo != 0 ? modelNo in checkLine()
|
/dports/science/jmol/jmol-14.32.7/src/org/jmol/quantum/ |
H A D | NMRCalculation.java | 122 BS bsModels = vwr.ms.getModelBS(bsA, false); in getInteractionTensorList() local 126 for (int i = bsModels.nextSetBit(0); i >= 0; i = bsModels.nextSetBit(i + 1)) { in getInteractionTensorList()
|
/dports/science/jmol/jmol-14.32.7/src/org/jmol/scriptext/ |
H A D | IsoExt.java | 905 BS bsModels = vwr.getVisibleFramesBitSet(); in mo() local 927 bsModels.clearAll(); in mo() 928 bsModels.set(i0); in mo() 932 for (int iModel = bsModels.nextSetBit(0); iModel >= 0; iModel = bsModels in mo() 3017 BS bsModels = vwr.ms.getModelBS(bsSelect, false); in isosurface() local 3018 if (bsModels.cardinality() > 1) in isosurface()
|
H A D | CmdExt.java | 1242 BS bsModels = null; in compare() local 1245 bsModels = vwr.ms.getModelBS(bsFrom, false); in compare() 1246 bsFrames = new BS[bsModels.cardinality()]; in compare() 1247 for (int i = 0, iModel = bsModels.nextSetBit( in compare() 1248 0); iModel >= 0; iModel = bsModels.nextSetBit(iModel + 1), i++) in compare() 1251 bsModels = BSUtil.newAndSetBit(0); in compare() 1254 …for (int iFrame = 0, iModel = bsModels.nextSetBit(0); iFrame < bsFrames.length; iFrame++, iModel =… in compare()
|
/dports/science/jmol/jmol-14.32.7/src/org/jmol/script/ |
H A D | ScriptEval.java | 4286 BS bsModels; in cmdLoad() local 4492 bsModels = (BS) getToken(i++).value; in cmdLoad() 4493 htParams.put("bsModels", bsModels); in cmdLoad() 4494 loadScript.append(" " + Escape.eBS(bsModels)); in cmdLoad()
|